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mol.spec.ts 6.80 KiB
/**
* Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
*/
import { parseMol, formalChargeMapper } from '../mol/parser';
const MolString = `2244
-OEChem-04072009073D
21 21 0 0 0 0 0 0 0999 V2000
1.2333 0.5540 0.7792 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6952 -2.7148 -0.7502 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7958 -2.1843 0.8685 O 0 0 0 0 0 0 0 0 0 0 0 0
1.7813 0.8105 -1.4821 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.0857 0.6088 0.4403 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7927 -0.5515 0.1244 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7288 1.8464 0.4133 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1426 -0.4741 -0.2184 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0787 1.9238 0.0706 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7855 0.7636 -0.2453 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1409 -1.8536 0.1477 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1094 0.6715 -0.3113 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5305 0.5996 0.1635 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1851 2.7545 0.6593 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.7247 -1.3605 -0.4564 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5797 2.8872 0.0506 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.8374 0.8238 -0.5090 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7290 1.4184 0.8593 H 0 0 0 0 0 0 0 0 0 0 0 0
4.2045 0.6969 -0.6924 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7105 -0.3659 0.6426 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2555 -3.5916 -0.7337 H 0 0 0 0 0 0 0 0 0 0 0 0
1 5 1 0 0 0 0
1 12 1 0 0 0 0
2 11 1 0 0 0 0
2 21 1 0 0 0 0
3 11 2 0 0 0 0
4 12 2 0 0 0 0
5 6 1 0 0 0 0
5 7 2 0 0 0 0
6 8 2 0 0 0 0
6 11 1 0 0 0 0
7 9 1 0 0 0 0
7 14 1 0 0 0 0
8 10 1 0 0 0 0
8 15 1 0 0 0 0
9 10 2 0 0 0 0
9 16 1 0 0 0 0
10 17 1 0 0 0 0
12 13 1 0 0 0 0
13 18 1 0 0 0 0
13 19 1 0 0 0 0
13 20 1 0 0 0 0
M END`;
const MolStringWithAtomBlockCharge = `
Ketcher 1 72215442D 1 1.00000 0.00000 0
4 3 0 0 0 0 999 V2000
0.0000 0.0000 0.0000 C 0 1 0 0 0 0 0 0 0 0 0 0
0.8660 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.8660 0.5000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.0000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
1 4 2 0 0 0 0
3 1 1 0 0 0 0
2 1 1 0 0 0 0
M END`;
const MolStringWithPropertyBlockCharge = `
Ketcher 1 72215442D 1 1.00000 0.00000 0
4 3 0 0 0 0 999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8660 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.8660 0.5000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.0000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
1 4 2 0 0 0 0
3 1 1 0 0 0 0
2 1 1 0 0 0 0
M CHG 3 2 -1 3 1 4 1
M END`;
const MolStringWithMultipleChargeLines = `
Ketcher 1 72215442D 1 1.00000 0.00000 0
4 3 0 0 0 0 999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8660 0.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.8660 0.5000 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.0000 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
1 4 2 0 0 0 0
3 1 1 0 0 0 0
2 1 1 0 0 0 0
M CHG 1 2 -1
M CHG 2 3 1 4 1
M END`;
describe('mol reader', () => {
it('basic', async () => {
const parsed = await parseMol(MolString).run();
if (parsed.isError) {
throw new Error(parsed.message);
}
const { atoms, bonds } = parsed.result;
// number of structures
expect(atoms.count).toBe(21);
expect(bonds.count).toBe(21);
expect(atoms.x.value(0)).toBeCloseTo(1.2333, 0.001);
expect(atoms.y.value(0)).toBeCloseTo(0.5540, 0.0001);
expect(atoms.z.value(0)).toBeCloseTo(0.7792, 0.0001);
expect(atoms.type_symbol.value(0)).toBe('O');
expect(bonds.atomIdxA.value(20)).toBe(13);
expect(bonds.atomIdxB.value(20)).toBe(20);
expect(bonds.order.value(20)).toBe(1);
});
it('property block charges', async () => {
const parsed = await parseMol(MolStringWithPropertyBlockCharge).run();
if (parsed.isError) {
throw new Error(parsed.message);
}
const { formalCharges } = parsed.result;
expect(formalCharges.atomIdx.rowCount).toBe(3);
expect(formalCharges.charge.rowCount).toBe(3);
expect(formalCharges.atomIdx.value(0)).toBe(2);
expect(formalCharges.atomIdx.value(1)).toBe(3);
expect(formalCharges.charge.value(0)).toBe(-1);
expect(formalCharges.charge.value(1)).toBe(1);
});
it('multiple charge lines', async () => {
const parsed = await parseMol(MolStringWithMultipleChargeLines).run();
if (parsed.isError) { throw new Error(parsed.message);
}
const { formalCharges } = parsed.result;
expect(formalCharges.atomIdx.rowCount).toBe(3);
expect(formalCharges.charge.rowCount).toBe(3);
expect(formalCharges.atomIdx.value(0)).toBe(2);
expect(formalCharges.atomIdx.value(1)).toBe(3);
expect(formalCharges.charge.value(0)).toBe(-1);
expect(formalCharges.charge.value(1)).toBe(1);
});
it('atom block charge mapping', async () => {
expect(formalChargeMapper(7)).toBe(-3);
expect(formalChargeMapper(6)).toBe(-2);
expect(formalChargeMapper(5)).toBe(-1);
expect(formalChargeMapper(0)).toBe(0);
expect(formalChargeMapper(3)).toBe(1);
expect(formalChargeMapper(2)).toBe(2);
expect(formalChargeMapper(1)).toBe(3);
expect(formalChargeMapper(4)).toBe(0);
});
it('atom block charges', async () => {
const parsed = await parseMol(MolStringWithAtomBlockCharge).run();
if (parsed.isError) {
throw new Error(parsed.message);
}
const { atoms, formalCharges } = parsed.result;
/* No property block charges */
expect(formalCharges.atomIdx.rowCount).toBe(0);
expect(formalCharges.charge.rowCount).toBe(0);
expect(atoms.formal_charge.value(0)).toBe(1);
expect(atoms.formal_charge.value(1)).toBe(0);
expect(atoms.formal_charge.value(2)).toBe(0);
expect(atoms.formal_charge.value(3)).toBe(0);
});
});